Normally I would say unless you are a beginner, stick with OF given Red Sail's rep. But if they have really changed for the better and I was staying at the Reef or Morritts, maybe I'd check them out. (I was at Morritt's last summer and dove with OF, as I had not heard anything different about RS at the point we booked.)
From the Reef you have to wander over to Morritt's next door, and even though I was staying there I'm still not sure what/where their current gear storage or handling situation is - I'd love if someone could describe? So it may or may not actually be any more convenient than driving a few minutes to Compass Point where they will clean/store your gear and have it waiting on the boat for you.)
IIRC OF used to do one tank trips in the afternoon but they changed to 2 tanks 1-2 years ago, and I'm pretty sure we did deep/shallow in the afternoon similar to the morning trips. (I'm just speculating but I'd guess they did this to increase capacity.) So while morning is still more popular, I think that's more a matter of freeing up the afternoons to do other things for some folks. Or maybe habit. But nothing wrong with sleeping in and doing the afternoon boats. Doing both am and pm boats there can be tight, so running back to your room between may not be on option if staying elsewhere. Not that you have that problem this time.
We were there when hurricane Ernesto went by and OF couldn't use their dock for a couple days. Think pretty much everyone lost at least a couple days of diving. As far as one being more sheltered than the other not really, just the luck of the draw.